Literature DB >> 18793125

Modelling cellular signalling systems.

Padmini Rangamani1, Ravi Iyengar.   

Abstract

Cell signalling pathways and networks are complex and often non-linear. Signalling pathways can be represented as systems of biochemical reactions that can be modelled using differential equations. Computational modelling of cell signalling pathways is emerging as a tool that facilitates mechanistic understanding of complex biological systems. Mathematical models are also used to generate predictions that may be tested experimentally. In the present chapter, the various steps involved in building models of cell signalling pathways are discussed. Depending on the nature of the process being modelled and the scale of the model, different mathematical formulations, ranging from stochastic representations to ordinary and partial differential equations are discussed. This is followed by a brief summary of some recent modelling successes and the state of future models.

Mesh:

Year:  2008        PMID: 18793125      PMCID: PMC3270941          DOI: 10.1042/BSE0450083

Source DB:  PubMed          Journal:  Essays Biochem        ISSN: 0071-1365            Impact factor:   8.000


  40 in total

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2.  Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors.

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Journal:  Nat Biotechnol       Date:  2002-04       Impact factor: 54.908

3.  A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (MAPK) pathway model.

Authors:  A R Asthagiri; D A Lauffenburger
Journal:  Biotechnol Prog       Date:  2001 Mar-Apr

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Journal:  Biophys J       Date:  2003-03       Impact factor: 4.033

5.  Signal transduction. History matters.

Authors:  Nicholas T Ingolia; Andrew W Murray
Journal:  Science       Date:  2002-08-09       Impact factor: 47.728

6.  MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network.

Authors:  Upinder S Bhalla; Prahlad T Ram; Ravi Iyengar
Journal:  Science       Date:  2002-08-09       Impact factor: 47.728

7.  Regulation of actin dynamics in rapidly moving cells: a quantitative analysis.

Authors:  Alex Mogilner; Leah Edelstein-Keshet
Journal:  Biophys J       Date:  2002-09       Impact factor: 4.033

Review 8.  PIP(2) and proteins: interactions, organization, and information flow.

Authors:  Stuart McLaughlin; Jiyao Wang; Alok Gambhir; Diana Murray
Journal:  Annu Rev Biophys Biomol Struct       Date:  2001-10-25

9.  The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responses.

Authors:  Christoph P Bagowski; Jaya Besser; Christian R Frey; James E Ferrell
Journal:  Curr Biol       Date:  2003-02-18       Impact factor: 10.834

10.  Competing docking interactions can bring about bistability in the MAPK cascade.

Authors:  Stefan Legewie; Birgit Schoeberl; Nils Blüthgen; Hanspeter Herzel
Journal:  Biophys J       Date:  2007-05-25       Impact factor: 4.033

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  10 in total

Review 1.  Impact of host genetic polymorphisms on vaccine induced antibody response.

Authors:  Janina E Linnik; Adrian Egli
Journal:  Hum Vaccin Immunother       Date:  2016-01-25       Impact factor: 3.452

Review 2.  Receptors, endocytosis, and trafficking: the biological basis of targeted delivery of antisense and siRNA oligonucleotides.

Authors:  R L Juliano; K Carver; C Cao; X Ming
Journal:  J Drug Target       Date:  2012-11-19       Impact factor: 5.121

Review 3.  Computational approaches for translational clinical research in disease progression.

Authors:  Mary F McGuire; Madurai Sriram Iyengar; David W Mercer
Journal:  J Investig Med       Date:  2011-08       Impact factor: 2.895

4.  Paradoxical signaling regulates structural plasticity in dendritic spines.

Authors:  Padmini Rangamani; Michael G Levy; Shahid Khan; George Oster
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-22       Impact factor: 11.205

5.  A multiscale model of the regulation of aquaporin 2 recycling.

Authors:  Christoph Leberecht; Michael Schroeder; Dirk Labudde
Journal:  NPJ Syst Biol Appl       Date:  2022-05-09

6.  A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation.

Authors:  Satya Nanda Vel Arjunan; Masaru Tomita
Journal:  Syst Synth Biol       Date:  2009-12-10

7.  Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Authors:  Jonathan R Karr; Alex H Williams; Jeremy D Zucker; Andreas Raue; Bernhard Steiert; Jens Timmer; Clemens Kreutz; Simon Wilkinson; Brandon A Allgood; Brian M Bot; Bruce R Hoff; Michael R Kellen; Markus W Covert; Gustavo A Stolovitzky; Pablo Meyer
Journal:  PLoS Comput Biol       Date:  2015-05-28       Impact factor: 4.475

8.  A predictive computational model reveals that GIV/girdin serves as a tunable valve for EGFR-stimulated cyclic AMP signals.

Authors:  Michael Getz; Lee Swanson; Debashish Sahoo; Pradipta Ghosh; Padmini Rangamani
Journal:  Mol Biol Cell       Date:  2019-04-24       Impact factor: 4.138

9.  A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ.

Authors:  Daniel Yakubovich; Shai Berlin; Uri Kahanovitch; Moran Rubinstein; Isabella Farhy-Tselnicker; Boaz Styr; Tal Keren-Raifman; Carmen W Dessauer; Nathan Dascal
Journal:  PLoS Comput Biol       Date:  2015-11-06       Impact factor: 4.475

10.  A dynamical systems model of progesterone receptor interactions with inflammation in human parturition.

Authors:  Douglas Brubaker; Alethea Barbaro; Mark R Chance; Sam Mesiano
Journal:  BMC Syst Biol       Date:  2016-08-19
  10 in total

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